My own little dark head-theory is that when the people of Skyloft came to settle the land, they carried diseases / bacteria / viruses with them that, while generally harmless to Hylians, wrecked havoc on the Mogmas. This stuff didn't affect the Gorons because Gorons are rock/mineral lifeforms and it didn't affect Kikwis because they're part-plant. It may or may not have affected Parella (but probably not because they're fish-type creatures)... Hylians and Mogmas, howevere, are both warm-blooded mammals and thus have more potential to pass sicknesses onto each other...
Think about history: When Europeans came to the North American contenient, they carried diseases that wiped out many of the native populations they came into contact with (this is beside the actual violence). So, I think, maybe people coming from "beyond the cloud barrier" might be immune to and carry things that the landlocked people are not immune to.
Erk, I know this is too morbid for Nintendo, so the Mogmas probably actually did go off to seek new treasure-lands or went to Holodrum to evolve into Subrosians or something.